The aim of this study was to assess the efficacy and tolerability of balneotherapy (BT) in patients with primary fibromyalgia syndrome (FS). In a prospective, randomized, controlled, double-blind trial with a 6-month follow-up, 100 FS patients were randomized to receive a cycle of BT with highly mineralized sulfate water (BT group) or with tap water (control group). Clinical assessments were performed at screening visit, at basal time, and after treatment (2 weeks, 3 and 6 months). The primary outcome measures were the change of global pain on the Visual Analogue Scale (VAS) and Fibromyalgia Impact Questionnaire total score (FIQ-Total) from baseline to 15 days. Secondary outcomes included Widespread Pain Index, Symptom Severity Scale Score, Short Form Health Survey, State-Trait Anxiety Inventory (STAI), and Center for Epidemiologic Studies Depression Scale. We performed an intent-to-treat analysis. The Kolmogorov-Smirnov test was applied to verify the normality distribution of all quantitative variables and the Student's t test to compare sample data. In the BT group, we observed a significant improvement of VAS and FIQ-Total at the end of the treatment that persisted until 6 months, while no significant differences were found in the control group. The differences between groups were significant for primary parameters at each time point. Similar results were obtained for the other secondary outcomes except for the STAI outcome. Adverse events were reported by 10 patients in the BT group and by 22 patients in the control group. Our results support the short- and long-term therapeutic efficacy of BT in FS.